RNA binding proteins (RBPs) are frequently targets of human autoimmune or genetic neurologic diseases. Notable examples among autoimmune disease include systemic lupus erythematosis, primary biliary cirrhosis (PBC) and Sjogren's syndrome, and among neurologic disease include the paraneoplastic neurologic antigens Nova and Hu, and the Fragile X mental retardation FMR1 protein, the spinal muscular atrophy SMN protein, the myotonic dystrophy CELF proteins, and the spinocerebellar ataxia SCA1 protein. Understanding the role these proteins play in disease, normal biology, and in the brain requires methods to identify the set of RNAs they bind to in vivo, and the use of mouse models of these disorders for RNA target validation. The targets of RBPs involved in a number of autoimmune and genetic diseases have been difficult to identify, however. Accordingly, the present invention provides methods for purifying RNA molecules interacting with an RNA